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Tool: Build Structure

The Build Structure tool builds and modifies atomic structures. The equivalent commands are build and bond. See also: Rotamers, Modeller Comparative, Model Loops, Altloc Explorer, Renumber Residues, rna, torsion

Build Structure can be opened from the Structure Editing section of the Tools menu and manipulated like other panels (more...). Sections:

Start Structure

The Start Structure section of Build Structure adds new atoms or molecules independent of any pre-existing atoms. See also: open, angle, torsion

Options to Add:

Modify Structure

The Modify Structure section of Build Structure can change the element, valence (number of directly attached atoms), and/or geometry (spatial arrangement of attached atoms) of a single selected atom at a time, potentially changing its atom type assignment. Hydrogens are appended as needed to fill the valence. Building outward can be done by successive cycles of modifying a hydrogen attached to the previously modified atom.

Clicking Apply changes the selected atom as specified:

Clicking the Delete button at the bottom of Modify Structure removes any selected atoms and bonds. See also command: delete, menu: Actions... Delete

Adjust Bonds

The Adjust Bonds section of Build Structure allows adding and deleting covalent bonds. A bond can also be deleted using its selection context menu. See also: bond, combine, delete

Join Models

The Join Models section of Build Structure allows forming a covalent bond between two atomic models to combine them into one. The atoms of one model are repositioned and incorporated into the other model; the original model will no longer exist. Thus, it may be a good idea to save a session beforehand, since the join (along with other building actions) cannot be undone. The related command combine also combines atomic models, but without forming a bond or changing the relative positions of the atoms.

The atoms to be bonded must first be selected.

Currently only a peptide bond can be formed. The selection must include exactly one peptide C-terminal carbon atom C OR N-terminal nitrogen atom N (not both) from one model, and from a second model, exactly one of whichever of those two atoms is not in the first. These C and N atoms each must be bonded to only one carbon (except N in proline or hydroxyproline can be bonded to two carbons); however, it may also be bonded to hydrogen and/or OXT, and if so, these atoms will be replaced as appropriate by the new peptide bond. The peptide bond will be added with the specified parameters:

Clicking Apply performs the join. The values of ω (omega), φ (phi), and other peptide torsion angles are attributes of the amino acid residue containing the newly bonded N.

Covalent Bond Radii

Approximate covalent bond radii are used to guess the connectivity of untemplated residues (when not specified in the input structure file) and to generate crude bond lengths for building atomic structures.

Selected covalent bond radii (Å)
H 0.23
B 0.83
C 0.68
N 0.68
O 0.68
F 0.64
Si 1.20
P 1.05
S 1.02
Cl 0.99
Se 1.22
Br 1.21
I 1.40

A complete list, obtained many years ago from documentation from the Cambridge Crystallographic Data Centre, can be found in Table III of:

Determination of molecular topology and atomic hybridization states from heavy atom coordinates. Meng EC, Lewis RA. J Comput Chem 12:891 (1991).

UCSF Resource for Biocomputing, Visualization, and Informatics / June 2022